LeishMicrosatDB: open source database of repeat sequences detected in six fully sequenced Leishmania genomes

• Published in: Database : the journal of biological databases and curation Vol. 2014; p. bau078
• Main Authors: Dikhit, Manas R, Moharana, Kanhu C, Sahoo, Bikash R, Sahoo, Ganesh C, Das, Pradeep
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 14.08.2014
• Subjects: Databases, Genetic; Genome, Protozoan - genetics; Genomics; Internet; Leishmania - genetics; Original; User-Computer Interface
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/bau078

A Leishmania Microsatellite Database (LeishMicrosatDB) is reported for genome wise mining of microsatellites in six Leishmania species, using in silico techniques. This was created to provide parasitologists a platform to understand the genome characterization, mapping, phylogeny and evolutionary analysis. The present version of the database contains 1,738,669 simple sequence repeats of which 181 s756 repeats are present in compound form. The repeats can be sought in a chromosome using input parameters such as repeat type (mono- hexa), coding status, repeat unit length and repeat sequence motif. The genic repeats have been further hyperlinked with their corresponding locus id, and the database is appended with primer3 plus for primer designing of selected repeats with left and right flanking sequences up to 250 bp. Information on clustering and polymorphic repeats can also be retrieved. This database may also be adopted as a tool to study the relative occurrence and distribution of microsatellites across the parasitic genome. The database can enable a biologist to select markers at desired intervals over the chromosomes, and can be accessed as an open source repository at http://biomedinformri.com/leishmicrosat. http://biomedinformri.com/leishmicrosat.